HEllo, 1. No. 2. No. 3. depends on the magnitude of the score, but tipically the lowest few scores do not represent meaningfully different models. reason for 1 and 2 is that modeller scores solely depend on the violation of restrainst, adding or removing some of them will setup a new relative pseudo-energy scale. best wishes, Andras Dan Thomas Major wrote: > > I have a few question concerning the energy terms computed by > MODELLER: > 1) Can the energy of a model computed with loop-modeling be compared > to the energy of a model computed without? > 2) Can the energy of a model with an additional constraint added (like > a specific distance constraint) be compared to the energy of a model > without that specific constraint? > 3) What kind of energy difference can be considered to reflect a > significant difference in the quality of models? > > Sincerely, > Dan Thomas Major > > -- > Dan Thomas Major (at Dr. B. Fischer's lab) > Bar-Ilan University > > Phone: 972-3-5317785 > Fax: 972-3-5348730 > > -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras